USDA-ARS Research Fellowship in Turfgrass Genomics

Research Project

During this project, you will be stationed at the Forage and Range Research Unit in Logan, UT, where you will explore the development of innovative tools for genome annotation and high-throughput genotyping of turfgrass plants with complex genomes. Guided by a mentor, you will have the opportunity to investigate the effectiveness of newly developed AI tools for gene annotation and compare them to current methods applied in complex turfgrass species. Through your participation, you will contribute to identifying and refining best practices for gene annotation in several turfgrass species. Additionally, you will collaborate with researchers in the ARS Turfgrass Working Group (TWG) to develop methods to call genotypes in polyploid grasses and format results for gene association studies. You will engage in evaluating software designed to produce robust genotypes in polyploids, both with and without imputation, and organize the optimized annotation and genotyping methods into containerized pipelines using tools like Docker and Singularity. These pipelines will be tailored for USDA ARS high-performance computing (HPC) clusters but will also be adaptable for broader use. As part of the project, you will help with the creation of documentation to support the scientific community in utilizing these pipelines effectively.

Learning Objectives

• Develop skills in genome annotation and genotyping in complex polyploid genomes
• Learn how to incorporate machine learning and AI into genomics research
• Develop skills in communicating and collaborating with scientists and staff in a group to advance research objectives
• Learn how to develop and publish containerized pipelines, documentation, and tutorials for use by other researchers

Mentor(s)

The mentor for this opportunity is Matthew Robbins (matthew.robbins@usda.gov). If you have questions about the nature of the research, please contact the mentor(s).

Citizenship Requirements

This opportunity is available to U.S. citizens only.

Qualifications

• The qualified candidate should have received a doctoral degree in one of the relevant fields (Plant Science, Bioinformatics, Computational Biology, Genetics, Genomics, or a related field of study). Degree must have been received within the past four years.
• Preferred skills:
• Knowledge of genome annotation and genotyping.
• Programming skills, such as Python and R.
• Skills in developing pipelines for genomic analyses.
• Knowledge and some experience in applying machine learning and AI to genomic analyses.
• Knowledge of plant science and polyploidy.

Contact Information

Please visit our Program Website. After reading, if you have additional questions about the application process, please email ORISE.ARS.HQPostdoc@orau.org and include the reference code for this opportunity.